We propose to organize a meeting titled Automated Function Prediction in the Summer of 2014 (AFP 2014). The meeting will consist of two components, the first being a series of talks (invited and contributed) and discussion sections dedicated to protein function research, with an emphasis on the theory and practice of computational methods utilized in functional annotation. The second component will provide a large-scale assessment of computational methods through participation in the 2nd Critical Assessment of Functional Annotation (CAFA), an experiment inspired by a highly-regarded CASP assessment protocol for protein structure prediction. Understanding protein function is critical to understanding life at the molecular level. It also provides important insights into understanding disease since many conditions arise as a consequence of the loss, disruption or gain of protein function. However, the rapidly growing number of sequenced organisms poses a challenge for functional genomics projects because of the need to experimentally annotate known proteins. Therefore, protein function prediction research is important for biomedical research. AFP 2014 will stimulate discussion and the exchange of ideas/experience regarding functional ontologies, experiments leading to functional annotations, biocuration, methodologies for predicting function, and effectiveness of these algorithms. The AFP 2014 meeting will be associated with the 22nd annual international conference on Intelligent Systems for Molecular Biology (ISMB), the official conference of the International Society for Computational Biology (ISCB). ISMB 2014 will be held in Boston, Massachusetts, in July of 2014, with AFP 2014 as a Special Interest Group meeting. This will not only ensure wide participation from the ISCB community, but also reduce costs compared to a stand-alone meeting. By organizing the CAFA challenge, we aim to not only assess the current methodology for function prediction, but also provide incentive for investigators to develop new and more accurate techniques that are necessary for the continuous progress of the field. The organizers of the meeting will strongly encourage broad participation of senior and junior scientists (including post-docs and students) as well as diversity. Collaboration is established with Jackson State University. Funding is requested for travel allowances only.